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Sample GSM651568 Query DataSets for GSM651568
Status Public on Jan 07, 2011
Title BE2_C-DS14635
Sample type RNA
 
Source name Human neuroblastoma
Organism Homo sapiens
Characteristics cell type: Human neuroblastoma
term: BTO:0000932
Biomaterial provider ATCC;CRL-2268
Treatment protocol For WI-38 cell type, Tamoxifen treated replicates only: induce senescence, cells at 50-80% confluency are treated for 72 hours with 20nM 4-hydroxytamoxifen in growth medium (from a 1000X working stock in absolute ethanol). At harvest, greater than 95% of DNA synthesis is inhibited and the cells have an induced fusiform/round morphology with greater than 95% showing dramatic senescence-associated heterochromatic foci
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
 
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymterix Gene Chip Scanner 3000
Description Human neuroblastoma
X_Hs_BE2c_E_101115_02_RS17238_W.CEL
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
 
Submission date Jan 07, 2011
Last update date Apr 23, 2013
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL5188
Series (1)
GSE19090 Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Data table header descriptions
ID_REF
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
ID_REF VALUE
2315101 112.7118
2315102 67.121
2315104 72.27731
2315105 20.79007
2315107 242.6598
2315112 129.7228
2315114 44.56224
2315116 56.26461
2315118 1188.266
2315120 430.5035
2315126 30.94236
2315132 5.277982E-05
2315138 117.2303
2315140 61.09445
2315142 17.17074
2315144 4.162367
2315146 38.73434
2315148 122.0182
2315149 189.9102
2315150 127.4439

Total number of rows: 1384231

Table truncated, full table size 22725 Kbytes.




Supplementary file Size Download File type/resource
GSM651568_X_Hs_BE2c_E_101115_02_RS17238_W.CEL.gz 23.5 Mb (ftp)(http) CEL
GSM651568_wgEncodeUwAffyExonArrayBe2cSimpleSignalRep2.broadPeak.gz 21.0 Mb (ftp)(http) BROADPEAK
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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